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  <span class="target" id="module-MDAnalysis.topology.__init__"></span><div class="section" id="topology-readers-mdanalysis-topology">
<h1>4.1. Topology readers &#8212; <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></tt><a class="headerlink" href="#topology-readers-mdanalysis-topology" title="Permalink to this headline">¶</a></h1>
<p>This submodule contains the topology readers. A topology file supplies the list
of atoms in the system, their connectivity and possibly additional information
such as B-factors, partial charges, etc. The details depend on the file format
and not every topology file provides all (or even any) additional data. As a
minimum, a topology file has to contain the names of atoms in the order of the
coordinate file and their residue names and numbers.</p>
<p>The following table lists the currently supported topology formats.</p>
<table border="1" class="docutils" id="supported-topology-formats">
<caption>Table of Supported topology formats</caption>
<colgroup>
<col width="17%" />
<col width="13%" />
<col width="70%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Name</th>
<th class="head">extension</th>
<th class="head">remarks</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>CHARMM/XPLOR</td>
<td>psf</td>
<td>reads either format, but only atoms and bonds
information is used at the moment;
<a class="reference internal" href="PSFParser.html#module-MDAnalysis.topology.PSFParser" title="MDAnalysis.topology.PSFParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PSFParser</span></tt></a></td>
</tr>
<tr><td>CHARMM*</td>
<td>crd</td>
<td>&#8220;CARD&#8221; coordinate output from CHARMM; deals with
either standard or EXTended format;
<a class="reference internal" href="CRDParser.html#module-MDAnalysis.topology.CRDParser" title="MDAnalysis.topology.CRDParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.CRDParser</span></tt></a></td>
</tr>
<tr><td>Brookhaven*</td>
<td>pdb</td>
<td>a simplified PDB format (as used in MD simulations)
is read by default; the full format can be read by
supplying the <cite>permissive=False</cite> flag to
<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>;
<a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></tt></a> and
<a class="reference internal" href="PDBParser.html#module-MDAnalysis.topology.PDBParser" title="MDAnalysis.topology.PDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PDBParser</span></tt></a></td>
</tr>
<tr><td>PQR*</td>
<td>pqr</td>
<td>PDB-like but whitespace-separated files with charge
and radius information;
<a class="reference internal" href="PQRParser.html#module-MDAnalysis.topology.PQRParser" title="MDAnalysis.topology.PQRParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PQRParser</span></tt></a></td>
</tr>
<tr><td>PDBQT*</td>
<td>pdbqt</td>
<td>file format used by AutoDock with atom types <em>t</em>
and partial charges <em>q</em>. Module:
<tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PQBQTParser</span></tt></td>
</tr>
<tr><td>GROMOS96*</td>
<td>gro</td>
<td>GROMOS96 coordinate file;
<a class="reference internal" href="GROParser.html#module-MDAnalysis.topology.GROParser" title="MDAnalysis.topology.GROParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.GROParser</span></tt></a></td>
</tr>
<tr><td>Amber</td>
<td>top
prmtop</td>
<td>simple Amber format read (only supports a subset of
flags);
<a class="reference internal" href="TOPParser.html#module-MDAnalysis.topology.TOPParser" title="MDAnalysis.topology.TOPParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TOPParser</span></tt></a></td>
</tr>
</tbody>
</table>
<p>Formats marked with ans asterisk * also hold coordinates and thus can
be used as the sole argument to <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> to set up
a system.</p>
<div class="admonition-see-also admonition seealso">
<p class="first admonition-title">See also</p>
<p class="last"><a class="reference internal" href="../coordinates_modules.html#coordinates"><em>Coordinates modules</em></a> with the <a class="reference internal" href="../coordinates/init.html#id1"><em>Table of Supported coordinate formats</em></a></p>
</div>
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